Rename AMReXParticleData to AMReXParticle

docs/amrex_data.ipynb

@@ -36,7 +36,7 @@
     "from flekspy.util import download_testfile, unit_one\n",
     "from flekspy.util.transformations import create_field_transform\n",
     "from flekspy.util.gmm import generate_synthetic_gmm_data, compare_gmm_results\n",
-    "from flekspy.amrex import AMReXParticleData\n",
+    "from flekspy.amrex import AMReXParticle\n",
     "\n",
     "import numpy as np\n",
     "import matplotlib.pyplot as plt\n",
@@ -77,7 +77,7 @@
    "source": [
     "## Using the Native AMReX Particle Loader\n",
     "\n",
-    "For scenarios where you only need to load particle data and the overhead of `yt` is not desired, `flekspy` provides a direct, experimental loader called `AMReXParticleData`. This is much faster than the yt loader with a simple interface."
+    "For scenarios where you only need to load particle data and the overhead of `yt` is not desired, `flekspy` provides a direct, experimental loader called `AMReXParticle`. This is much faster than the yt loader with a simple interface."
    ]
   },
   {
@@ -87,7 +87,7 @@
    "outputs": [],
    "source": [
     "data_file = \"data/3d_particle_region0_1_t00000002_n00000007_amrex\"\n",
-    "pd = AMReXParticleData(data_file)\n",
+    "pd = AMReXParticle(data_file)\n",
     "pd"
    ]
   },

samples/vdf_matrix.py

@@ -42,7 +42,7 @@ def calculate_histograms(particle_file, regions, var_x, var_y, hist_range, hist_
     """
     print(f"Loading particle data from: {particle_file}")
     try:
-        pd = flekspy.amrex.AMReXParticleData(particle_file)
+        pd = flekspy.amrex.AMReXParticle(particle_file)
     except Exception as e:
         print(f"Error loading particle data: {e}")
         return [], 0.0  # Return empty list and zero max

src/flekspy/__init__.py

@@ -14,7 +14,7 @@
     "YtFLEKSData",
     "extract_phase",
     "FLEKSTP",
-    "AMReXParticleData",
+    "AMReXParticle",
     "xr",
 ]
 
@@ -27,7 +27,7 @@ def __getattr__(name):
         "YtFLEKSData": "flekspy.yt",
         "extract_phase": "flekspy.yt",
         "FLEKSTP": "flekspy.tp",
-        "AMReXParticleData": "flekspy.amrex",
+        "AMReXParticle": "flekspy.amrex",
         "read_idl": "flekspy.idl",
         "DerivedAccessor": "flekspy.idl",
         "xr": "xarray",
@@ -95,7 +95,7 @@ def load(
             YtFLEKSData = __getattr__("YtFLEKSData")
             return YtFLEKSData(filename, readFieldData)
         else:
-            AMReXParticleData = __getattr__("AMReXParticleData")
-            return AMReXParticleData(filename)
+            AMReXParticle = __getattr__("AMReXParticle")
+            return AMReXParticle(filename)
     else:
         raise Exception("Error: unknown file format!")

src/flekspy/amrex/__init__.py

@@ -1,3 +1,3 @@
-from .particle_data import AMReXParticleData, AMReXParticleHeader
+from .particle_data import AMReXParticle, AMReXParticleHeader
 
-__all__ = ["AMReXParticleData", "AMReXParticleHeader"]
+__all__ = ["AMReXParticle", "AMReXParticleHeader"]

src/flekspy/amrex/particle_data.py

@@ -165,7 +165,7 @@ def read_amrex_binary_particle_file(
     return idata, rdata
 
 
-class AMReXParticleData(AMReXPlottingMixin):
+class AMReXParticle(AMReXPlottingMixin):
     """
     This class provides an interface to the particle data in a plotfile.
     Data is loaded lazily upon first access to `idata` or `rdata`.
@@ -279,7 +279,7 @@ def _parse_particle_h_files(self) -> None:
 
     def __repr__(self) -> str:
         repr_str = (
-            f"AMReXParticleData from {self.output_dir}\n"
+            f"AMReXParticle from {self.output_dir}\n"
             f"Time: {self.time}\n"
             f"Dimensions: {self.dim}\n"
             f"Domain Dimensions: {self.domain_dimensions}\n"

src/flekspy/amrex/plotting.py

@@ -9,7 +9,7 @@
 
 
 class AMReXPlottingMixin:
-    """A mixin class for AMReXParticleData plotting functionalities."""
+    """A mixin class for AMReXParticle plotting functionalities."""
 
     _AXIS_LABEL_MAP = {
         "velocity_x": r"$v_x$",

tests/test_amrex_3d_plots.py

@@ -1,7 +1,7 @@
 import pytest
 from unittest.mock import patch
 import matplotlib.pyplot as plt
-from flekspy.amrex import AMReXParticleData
+from flekspy.amrex import AMReXParticle
 from pathlib import Path
 
 @pytest.mark.parametrize(
@@ -18,7 +18,7 @@ def test_3d_plots(setup_test_data, data_file, plot_method_name):
     a matplotlib figure and axes.
     """
     data_dir = Path(setup_test_data)
-    ds = AMReXParticleData(data_dir / data_file)
+    ds = AMReXParticle(data_dir / data_file)
     plot_func = getattr(ds, plot_method_name)
 
     with patch("matplotlib.pyplot.show"):

tests/test_amrex_loader.py

@@ -1,5 +1,5 @@
 import pytest
-from flekspy.amrex import AMReXParticleData
+from flekspy.amrex import AMReXParticle
 from flekspy.amrex.plotting import AMReXPlottingMixin
 import numpy as np
 import matplotlib.pyplot as plt
@@ -19,7 +19,7 @@ def select_particles_in_region(self, x_range=None, y_range=None, z_range=None):
 
 @pytest.fixture
 def mock_amrex_data():
-    """Creates a mock AMReXParticleData object for testing."""
+    """Creates a mock AMReXParticle object for testing."""
     # Mock header
     header = MagicMock()
     header.real_component_names = ["x", "y", "z", "velocity_x", "velocity_y", "velocity_z", "weight"]
@@ -37,7 +37,7 @@ def particle_data(setup_test_data):
     plotfile_directory = os.path.join(
         setup_test_data, "3d_particle_region0_1_t00000002_n00000007_amrex"
     )
-    return AMReXParticleData(plotfile_directory)
+    return AMReXParticle(plotfile_directory)
 
 
 @pytest.fixture
@@ -68,8 +68,8 @@ def mock_plot_components():
 
 @pytest.fixture
 def mock_pdata():
-    """Provides a mock AMReXParticleData object with alias resolution mocked."""
-    pdata = MagicMock(spec=AMReXParticleData)
+    """Provides a mock AMReXParticle object with alias resolution mocked."""
+    pdata = MagicMock(spec=AMReXParticle)
     pdata._resolve_alias.side_effect = lambda x: x
     pdata._get_axis_label.side_effect = lambda x: x
     return pdata
@@ -135,7 +135,7 @@ def test_plot_phase(mock_plot_components, mock_pdata):
         "Normalized Weighted Density",
     )
 
-    result_fig, result_ax = AMReXParticleData.plot_phase(
+    result_fig, result_ax = AMReXParticle.plot_phase(
         mock_pdata,
         x_variable="x",
         y_variable="vy",
@@ -180,7 +180,7 @@ def test_plot_phase_with_existing_axes(mock_plot_components, mock_pdata):
         "Particle Count",
     )
 
-    result_fig, result_ax = AMReXParticleData.plot_phase(
+    result_fig, result_ax = AMReXParticle.plot_phase(
         mock_pdata, x_variable="x", y_variable="y", ax=mock_ax
     )
 
@@ -203,7 +203,7 @@ def test_plot_phase_no_colorbar(mock_plot_components, mock_pdata):
         "Particle Count",
     )
 
-    AMReXParticleData.plot_phase(
+    AMReXParticle.plot_phase(
         mock_pdata, x_variable="x", y_variable="y", add_colorbar=False
     )
 
@@ -217,7 +217,7 @@ def test_plot_phase_no_particles(mock_plot_components, mock_pdata):
     """
     mock_pdata.get_phase_space_density.return_value = None
 
-    result = AMReXParticleData.plot_phase(
+    result = AMReXParticle.plot_phase(
         mock_pdata, x_variable="x", y_variable="y", x_range=(0, 1)
     )
 
@@ -237,7 +237,7 @@ def test_plot_phase_with_hist_range(mock_plot_components, mock_pdata):
     )
 
     custom_range = [[0.1, 0.9], [0.2, 0.8]]
-    AMReXParticleData.plot_phase(
+    AMReXParticle.plot_phase(
         mock_pdata, x_variable="x", y_variable="y", hist_range=custom_range
     )
 
@@ -259,7 +259,7 @@ def test_plot_phase_log_scale_with_vmin_vmax(mock_plot_components, mock_pdata):
     )
 
     with patch("matplotlib.colors.LogNorm") as mock_log_norm:
-        AMReXParticleData.plot_phase(
+        AMReXParticle.plot_phase(
             mock_pdata, x_variable="x", y_variable="y", log_scale=True, vmin=1, vmax=10
         )
         mock_log_norm.assert_called_once_with(vmin=1, vmax=10)
@@ -287,7 +287,7 @@ def test_plot_phase_subplots(mock_pdata):
     with patch(
         "matplotlib.pyplot.subplots", return_value=(fig_mock, axes_mock)
     ) as mock_subplots:
-        result_fig, result_axes = AMReXParticleData.plot_phase_subplots(
+        result_fig, result_axes = AMReXParticle.plot_phase_subplots(
             mock_pdata,
             x_variable="x",
             y_variable="vy",
@@ -337,7 +337,7 @@ def test_plot_phase_subplots_empty_region(mock_pdata):
         "matplotlib.pyplot.subplots", return_value=(fig_mock, axes_mock)
     ):
         # This should execute without raising a ValueError
-        AMReXParticleData.plot_phase_subplots(
+        AMReXParticle.plot_phase_subplots(
             mock_pdata,
             x_variable="x",
             y_variable="vy",
@@ -421,7 +421,7 @@ def test_plot_phase_with_transform(mock_plot_components, mock_pdata):
     def dummy_transform(data):
         return data, ["x_new", "y_new"]
 
-    AMReXParticleData.plot_phase(
+    AMReXParticle.plot_phase(
         mock_pdata,
         x_variable="x_new",
         y_variable="y_new",
@@ -446,7 +446,7 @@ def test_plot_phase_with_kde(mock_plot_components, mock_pdata):
         "Weighted Density",
     )
 
-    AMReXParticleData.plot_phase(
+    AMReXParticle.plot_phase(
         mock_pdata,
         x_variable="x",
         y_variable="y",
@@ -488,7 +488,7 @@ def test_plot_phase_with_spatial_transform(mock_plot_components, mock_pdata):
     def spatial_transform(data):
         return data, ["pos_parallel", "pos_perp"]
 
-    AMReXParticleData.plot_phase(
+    AMReXParticle.plot_phase(
         mock_pdata,
         x_variable="pos_parallel",
         y_variable="pos_perp",
@@ -521,7 +521,7 @@ def field_aligned_transform(data):
             "v_perp1",
         ]
 
-    AMReXParticleData.plot_phase(
+    AMReXParticle.plot_phase(
         mock_pdata,
         x_variable="v_parallel",
         y_variable="v_perp1",
@@ -546,7 +546,7 @@ def test_get_phase_space_density_basic(mock_pdata):
             np.array([0.0, 1.0]),
             np.array([0.0, 1.0]),
         )
-        H, xedges, yedges, cbar_label = AMReXParticleData.get_phase_space_density(
+        H, xedges, yedges, cbar_label = AMReXParticle.get_phase_space_density(
             mock_pdata, x_variable="x", y_variable="y"
         )
 
@@ -566,7 +566,7 @@ def test_get_phase_space_density_normalized(mock_pdata):
     # and get_phase_space_density will use mock_pdata.rdata
     mock_pdata.select_particles_in_region.return_value = mock_pdata.rdata
 
-    H, _, _, cbar_label = AMReXParticleData.get_phase_space_density(
+    H, _, _, cbar_label = AMReXParticle.get_phase_space_density(
         mock_pdata, x_variable="x", y_variable="y", normalize=True
     )
 
@@ -590,7 +590,7 @@ def scale_transform(data):
             np.array([0.0, 1.0]),
             np.array([0.0, 1.0]),
         )
-        AMReXParticleData.get_phase_space_density(
+        AMReXParticle.get_phase_space_density(
             mock_pdata,
             x_variable="x_scaled",
             y_variable="y_scaled",
@@ -619,7 +619,7 @@ def test_get_phase_space_density_with_kde(mock_pdata):
         mock_kde_instance.return_value = np.random.rand(10 * 10)
         mock_gaussian_kde.return_value = mock_kde_instance
 
-        _, _, _, cbar_label = AMReXParticleData.get_phase_space_density(
+        _, _, _, cbar_label = AMReXParticle.get_phase_space_density(
             mock_pdata,
             x_variable="x",
             y_variable="y",
@@ -651,7 +651,7 @@ def mock_select(x_range=None, y_range=None, z_range=None):
 
     mock_pdata.select_particles_in_region.side_effect = mock_select
 
-    H, _, _, _ = AMReXParticleData.get_phase_space_density(
+    H, _, _, _ = AMReXParticle.get_phase_space_density(
         mock_pdata,
         x_variable="x",
         y_variable="y",
@@ -689,7 +689,7 @@ def test_plot_phase_with_marginals(mock_plot_components, mock_pdata):
         )
 
         with patch("matplotlib.pyplot.figure", return_value=mock_fig):
-            AMReXParticleData.plot_phase(
+            AMReXParticle.plot_phase(
                 mock_pdata, x_variable="x", y_variable="y", marginals=True
             )
 

tests/test_fleks.py

@@ -136,7 +136,7 @@ def test_amrex_plot(self, amrex_data_files):
 
     def test_amrex_particle_loader_default(self, setup_test_data):
         ds = fs.load(os.path.join(setup_test_data, "3d_particle*amrex"))
-        assert isinstance(ds, fs.amrex.AMReXParticleData)
+        assert isinstance(ds, fs.amrex.AMReXParticle)
 
 
 @pytest.fixture(scope="class")

tests/test_gmm_parameters.py

@@ -4,7 +4,7 @@
 from unittest.mock import MagicMock
 
 from flekspy.util.gmm import get_gmm_parameters
-from flekspy.amrex.particle_data import AMReXParticleData
+from flekspy.amrex.particle_data import AMReXParticle
 
 
 @pytest.fixture
@@ -54,7 +54,7 @@ def test_get_gmm_temperatures_isotropic(fitted_gmm):
     from scipy.constants import m_u, k
 
     # Test with explicit particle_mass in amu
-    parameters = AMReXParticleData.get_gmm_temperatures(
+    parameters = AMReXParticle.get_gmm_temperatures(
         fitted_gmm, particle_mass=2.0, isotropic=True
     )
 
@@ -68,7 +68,7 @@ def test_get_gmm_temperatures_isotropic(fitted_gmm):
     assert parameters[1]["temperature"] == pytest.approx(expected_temp_2)
 
     # Test with default particle_mass (should be 1.0 amu)
-    parameters_default = AMReXParticleData.get_gmm_temperatures(
+    parameters_default = AMReXParticle.get_gmm_temperatures(
         fitted_gmm, isotropic=True
     )
     expected_temp_1_default = 1.0 * m_u * 1.5 / k
@@ -87,7 +87,7 @@ def test_get_gmm_temperatures_bi_maxwellian(fitted_gmm):
     """
     from scipy.constants import m_u, k
 
-    parameters = AMReXParticleData.get_gmm_temperatures(
+    parameters = AMReXParticle.get_gmm_temperatures(
         fitted_gmm, particle_mass=2.0, isotropic=False
     )